Contacts of the helix formed by residues 59 - 85 (chain A) in PDB entry 2OI8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.6 15.2 - - - +
54A TYR* 3.6 15.3 - - - -
57A PHE* 2.7 11.5 + - - +
58A ASP* 1.3 73.6 - - - +
60A ARG* 1.3 65.5 + - - -
61A ASP 3.2 4.8 + - - -
62A GLU* 3.2 13.7 + - - +
63A LEU* 3.3 8.5 + - - +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.8 25.1 + - - +
37A LEU* 3.2 31.9 - - + +
38A SER* 5.7 0.4 - - - -
39A LEU* 3.8 15.9 - - + +
54A TYR* 5.1 0.8 + - - -
59A GLY* 1.3 71.0 - - - -
61A ASP* 1.3 86.3 + - - +
63A LEU* 3.3 7.8 + - + +
64A ILE* 2.8 46.2 + - + +
115A VAL* 3.8 13.9 - - - +
116A PRO 3.2 26.3 + - - -
117A GLY* 4.5 2.4 - - - -
118A TYR* 4.2 6.8 - - - +
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY 3.2 1.2 + - - -
60A ARG* 1.3 103.1 + - - +
62A GLU* 1.3 54.7 + - - +
64A ILE* 3.2 0.3 + - - +
65A THR* 2.7 43.1 + - - +
117A GLY 4.7 4.2 - - - +
118A TYR* 3.2 39.4 - - + +
119A ARG 4.9 5.1 + - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR 4.8 0.9 - - - +
57A PHE* 3.8 13.5 - - + -
58A ASP* 3.1 49.0 + - - +
59A GLY 3.2 11.1 + - - +
61A ASP* 1.3 78.9 - - - +
63A LEU* 1.3 59.8 + - - +
65A THR* 3.7 6.6 - - - +
66A GLU* 3.2 27.0 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.5 4.3 - - + -
22A LYS* 4.0 16.4 - - + -
25A ALA* 3.9 22.7 - - + -
37A LEU* 4.3 17.3 - - + -
39A LEU* 3.9 23.8 - - + +
42A ILE* 4.5 5.8 - - + -
57A PHE* 3.7 43.0 - - + -
59A GLY 3.3 6.0 + - - +
60A ARG* 3.3 12.0 + - - +
61A ASP 3.2 0.4 - - - -
62A GLU* 1.3 75.7 - - - +
64A ILE* 1.3 67.2 + - - +
66A GLU* 3.2 3.3 + - - +
67A LEU* 3.0 32.1 + - + +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 4.8 13.9 - - + -
35A SER 5.1 0.2 - - - +
37A LEU* 3.3 33.2 - - + -
60A ARG* 2.8 41.7 + - + +
61A ASP* 3.6 6.5 - - - +
63A LEU* 1.3 74.5 - - - +
65A THR* 1.3 66.5 + - - +
67A LEU* 2.9 12.2 + - + +
68A ILE* 2.8 46.6 + - + +
109A LEU* 5.1 6.5 - - + -
115A VAL* 4.9 14.4 - - + -
118A TYR* 3.6 24.2 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 2.7 26.7 + - - +
62A GLU* 3.7 9.1 - - - +
64A ILE* 1.3 73.6 - - - +
66A GLU* 1.3 59.3 + - - +
68A ILE* 3.3 4.8 + - - +
69A ARG* 3.0 52.0 + - - +
118A TYR* 2.7 25.2 + - - +
121A PRO* 3.6 28.4 - - + +
123A ASP* 5.4 0.2 - - - +
124A ILE* 6.1 3.0 - - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 6.2 0.9 - - - +
22A LYS* 4.4 15.9 + - + +
57A PHE* 3.7 27.1 - - + -
62A GLU 3.2 8.5 + - - +
63A LEU 3.2 9.0 + - - +
65A THR* 1.3 78.2 - - - +
67A LEU* 1.3 60.1 + - - +
69A ARG* 3.4 40.9 + - - +
70A ASP* 2.9 41.9 + - - +
73A ARG* 4.7 2.8 + - - -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.8 37.5 - - + +
25A ALA* 4.0 16.4 - - + -
26A TRP* 3.5 31.4 - - + +
29A ILE* 3.8 28.3 - - + -
37A LEU* 4.4 9.4 - - + -
63A LEU* 3.0 21.4 + - + +
64A ILE* 2.9 10.6 + - + +
66A GLU* 1.3 75.8 - - - +
68A ILE* 1.3 58.1 + - - +
70A ASP* 3.3 7.1 + - - +
71A ALA* 2.9 30.0 + - - +
109A LEU* 3.8 15.2 - - + +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 2.8 38.2 + - + +
65A THR* 3.6 8.1 - - - +
67A LEU* 1.3 72.5 - - - +
69A ARG* 1.3 62.1 + - - +
71A ALA* 3.2 2.9 + - - +
72A TYR* 3.0 50.2 + - + -
109A LEU* 4.0 30.3 - - + +
110A ILE* 3.8 10.1 - - + -
115A VAL* 6.0 2.2 - - + -
118A TYR* 3.6 24.9 - - + +
120A ALA* 5.5 0.9 - - + -
124A ILE* 4.2 15.0 - - + -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 3.0 34.1 + - + +
66A GLU* 3.4 35.4 + - - +
67A LEU 3.4 0.2 - - - -
68A ILE* 1.3 72.5 - - - +
70A ASP* 1.3 59.9 + - - +
72A TYR* 3.4 9.1 + - - +
73A ARG* 3.0 59.7 + - - +
121A PRO* 4.9 2.0 - - - +
123A ASP* 2.7 38.3 + - - +
124A ILE* 6.0 2.9 - - - +
127A ILE* 5.4 11.1 - - + +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 2.8 42.6 + - - +
26A TRP* 5.5 6.7 + - + +
66A GLU* 2.9 19.5 + - - +
67A LEU* 3.5 8.9 - - - +
69A ARG* 1.3 76.2 - - - +
71A ALA* 1.3 62.4 + - - +
73A ARG* 3.3 24.7 + - - +
74A SER* 3.2 23.6 + - - -
106A ARG* 5.4 0.6 - - - -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 4.9 1.8 - - + -
67A LEU 2.9 13.6 + - - +
68A ILE* 3.2 9.4 + - - +
70A ASP* 1.3 74.3 - - - +
72A TYR* 1.3 63.9 + - - +
74A SER* 2.9 21.3 + - - -
75A GLN 3.1 7.4 + - - -
99A TRP* 3.6 9.3 - - + -
106A ARG* 3.7 28.5 - - + +
109A LEU* 4.7 5.6 - - + -
110A ILE* 3.7 23.3 - - + -
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.0 45.3 + - + -
69A ARG* 3.8 9.0 - - - +
71A ALA* 1.3 75.4 - - - +
73A ARG* 1.3 58.3 + - - +
75A GLN* 3.2 21.2 + - - +
76A ALA* 2.9 29.0 + - - +
110A ILE* 3.4 37.8 + - + +
111A PHE* 5.1 2.5 - + - -
124A ILE* 3.4 28.2 + - + -
125A THR* 5.7 1.0 - - - +
127A ILE* 3.8 21.0 - - + +
128A ALA* 3.9 25.3 - - + +
131A THR* 3.9 4.7 + - - -
180A TRP* 6.2 1.1 - + - -
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 4.7 3.6 + - - -
69A ARG* 3.0 54.1 + - - +
70A ASP* 3.5 28.0 + - - +
71A ALA 3.2 0.6 - - - -
72A TYR* 1.3 78.1 - - - +
74A SER* 1.3 57.1 + - - +
76A ALA* 3.4 6.1 + - - +
77A ASP* 2.9 46.6 + - - +
80A ARG* 5.3 4.0 - - - +
127A ILE* 5.9 3.2 - - - +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP 3.2 12.5 + - - -
71A ALA 2.9 15.1 + - - -
73A ARG* 1.3 74.1 - - - +
75A GLN* 1.3 65.1 + - - +
77A ASP* 3.7 10.3 - - - +
78A SER* 3.1 23.7 + - - -
99A TRP* 3.3 19.5 + - - -
106A ARG* 3.5 22.0 + - - -
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 3.1 8.2 + - - +
72A TYR* 3.2 21.7 + - - +
74A SER* 1.3 79.5 + - - +
76A ALA* 1.3 62.4 + - - +
78A SER* 3.5 3.1 + - - -
79A LEU* 3.2 24.4 + - + +
96A LEU* 3.5 21.4 - - + +
99A TRP* 3.3 35.2 - - + +
110A ILE* 5.8 0.2 - - - +
111A PHE* 3.3 29.5 - - - -
131A THR* 3.6 19.4 + - + +
180A TRP* 3.1 34.8 - - - -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR 2.9 13.5 + - - +
73A ARG* 3.6 8.1 - - - +
75A GLN* 1.3 75.5 - - - +
77A ASP* 1.3 55.4 + - - +
79A LEU* 3.7 1.7 - - - +
80A ARG* 2.8 58.6 + - + +
127A ILE 5.7 0.4 - - - +
130A GLU* 4.4 9.4 - - + -
131A THR* 3.4 30.7 + - - +
134A VAL* 5.5 0.4 - - - +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 2.9 37.1 + - - +
74A SER* 3.7 9.5 - - - +
75A GLN 3.3 0.4 - - - -
76A ALA* 1.3 72.7 - - - +
78A SER* 1.3 67.7 + - - +
80A ARG* 3.0 33.1 + - - +
81A ALA* 3.0 27.6 + - - +
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER 3.1 17.5 + - - -
75A GLN 3.6 5.4 - - - -
77A ASP* 1.3 79.3 - - - +
79A LEU* 1.3 63.5 + - - +
81A ALA* 3.5 5.5 + - - +
82A ALA* 3.3 18.9 + - - +
95A ALA* 3.3 30.7 + - - +
99A TRP* 3.8 18.4 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 3.2 16.5 + - + +
76A ALA* 3.9 3.6 - - - +
78A SER* 1.3 80.8 - - - +
80A ARG* 1.3 66.4 + - - +
82A ALA* 3.3 6.7 + - - +
83A ALA* 3.2 21.7 + - - +
92A LEU* 3.9 15.5 - - + +
95A ALA* 3.9 20.4 - - + -
96A LEU* 3.9 24.2 - - + +
131A THR* 3.3 34.3 - - + +
134A VAL* 3.9 13.2 - - + +
135A ILE* 3.8 26.9 - - + -
179A PHE* 5.8 0.7 - - + -
180A TRP* 4.7 6.3 - - + -
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 4.4 5.7 + - - +
76A ALA* 2.8 40.3 + - + +
77A ASP* 3.0 33.9 + - - +
79A LEU* 1.3 72.2 - - - +
81A ALA* 1.3 54.5 + - - +
83A ALA* 3.1 5.3 + - - +
84A ALA* 2.8 37.8 + - + +
130A GLU* 5.7 5.8 - - - +
134A VAL* 4.1 20.0 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP 3.0 17.2 + - - +
78A SER* 3.7 6.7 - - - +
80A ARG* 1.3 75.5 - - - +
82A ALA* 1.3 56.0 + - - +
84A ALA* 3.5 7.1 + - - +
85A SER* 3.0 29.3 + - - -
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 3.3 10.7 + - - +
79A LEU 3.3 5.8 + - - +
80A ARG 3.1 0.4 - - - -
81A ALA* 1.3 78.8 - - - +
83A ALA* 1.3 58.9 + - - +
85A SER* 3.1 11.3 + - - -
87A ALA* 3.0 34.1 + - + +
91A GLY 4.2 6.7 - - - +
92A LEU* 3.4 20.4 - - + -
95A ALA* 3.9 18.2 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 3.2 4.6 + - - -
80A ARG* 3.1 7.6 + - - +
82A ALA* 1.3 73.5 - - - +
84A ALA* 1.3 59.6 - - - +
86A GLY* 3.0 19.8 + - - -
87A ALA 4.3 7.8 - - - +
92A LEU* 3.7 9.1 - - + +
134A VAL* 3.7 29.6 - - + -
137A ASP* 6.4 0.9 - - + -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG 2.8 19.9 + - - +
81A ALA* 3.7 7.6 - - - +
83A ALA* 1.3 78.6 - - - +
85A SER* 1.3 55.0 + - - +
86A GLY 3.2 2.8 + - - -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA 3.0 15.4 + - - -
82A ALA* 3.1 15.1 + - - -
83A ALA 3.2 0.4 - - - -
84A ALA* 1.3 74.3 - - - +
86A GLY* 1.3 58.8 + - - +
87A ALA* 3.3 6.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il